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Background The terrestrial land surface in West Africa is made up several types of savanna ecosystems differing in land use changes which modulate gas exchanges between their vegetation and the overlying atmosphere. This study compares diurnal and seasonal estimates of CO2 fluxes from three contrasting ecosystems, a grassland, a mixture of fallow and cropland, and nature reserve in the Sudanian Savanna and relate them to water availability and land use characteristics. Results Over the study period, and for the three study sites, low soil moisture availability, high vapour pressure deficit and low ecosystem respiration were prevalent during the dry season (November to March), but the contrary occurred during the rainy season (May to October). Carbon uptake predominantly took place in the rainy season, while net carbon efflux occurred in the dry season as well as the dry to wet and wet to dry transition periods (AM and ND) respectively. Carbon uptake decreased in the order of the nature reserve, a mixture of fallow and cropland, and grassland. Only the nature reserve ecosystem at the Nazinga Park served as a net sink of CO2, mostly by virtue of a several times larger carbon uptake and ecosystem water use efficiency during the rainy season than at the other sites. These differences were influenced by albedo, LAI, EWUE, PPFD and climatology during the period of study. Conclusion These results suggest that land use characteristics affect plant physiological processes that lead to flux exchanges over the Sudanian Savanna ecosystems. It affects the diurnal, seasonal and annual changes in NEE and its composite signals, GPP and RE. GPP and NEE were generally related as NEE scaled with photosynthesis with higher CO2 assimilation leading to higher GPP. However, CO2 effluxes over the study period suggest that besides biomass regrowth, other processes, most likely from the soil might have also contributed to the enhancement of ecosystem respiration. [ABSTRACT FROM AUTHOR]